[phenixbb] special positions Refinement crash
Yarrow Madrona
amadrona at uci.edu
Thu Oct 10 08:55:42 PDT 2013
Thank you Pavel,
Even setting this value up to 10 didn't seem to fix the issue. It seems to
crash. log report is below.
=========================== Add C-beta restraints
============================
Adding C-beta torsion restraints...
num c-beta restraints: 732
==================== Compute data/restraints target weights
===================
Traceback (most recent call last):
File
"/usr/bin/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/refine.py",
line 11, in <module>
command_line.run(command_name="phenix.refine", args=sys.argv[1:])
File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/command_line.py",
line 159, in run
call_back_handler=call_back_handler)
File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py",
line 1593, in run
reference_model_manager = self.reference_model_manager).result
File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/strategies.py",
line 171, in __init__
ion_placement_manager = ion_placement_manager)
File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
line 87, in __init__
self.call(self.weight, "Compute data/restraints target weights")
File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
line 137, in call
func(prefix = prefix)
File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
line 302, in weight
log = self.log)
File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weights.py",
line 20, in run
log = log)
File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
line 368, in __init__
self.xyz_weights_result = self.xyz_weights()
File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
line 411, in xyz_weights
log=self.log)
File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
line 294, in __init__
verbose=0)
File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/memory_eraser.py",
line 29, in shake_sites
max_iterations = max_iterations))
File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
line 43, in __init__
exception_handling_params=lbfgs_exception_handling_params)
File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py",
line 259, in run
log)
File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py",
line 127, in run_c_plus_plus
f, g = target_evaluator.compute_functional_and_gradients()
File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
line 89, in compute_functional_and_gradients
self.apply_shifts()
File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
line 70, in apply_shifts
site_cart=self.tmp.sites_shifted[i_seq])
File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/__init__.py",
line 609, in correct_special_position
raise AssertionError(error_message)
AssertionError: Excessive special position correction:
unit_cell: (56.278, 67.256, 106.26, 90, 90, 90)
space_group_info: P 21 2 2
special_op: 1/2,y,1/2
site_frac: (0.5155158345734757, 0.37698455671246006, 0.504900074345152)
site_special_frac: (0.5, 0.37698455671246006, 0.5)
distance_moved: 1.01666
udp021848uds:Refine_P2122 yarrowmadrona$
> Hi Yarrow,
>
> please try increasing this parameter (default is 1.0)
>
> correct_special_position_tolerance
>
> and let me know if this does not help. Set to 2 or so.
>
> Pavel
>
> On 10/9/13 4:17 PM, Yarrow Madrona wrote:
>> Hello,
>>
>> I am trying to do a refinement and I get an error that I think means I
>> have atoms on special positions. The refinement stops and gives the
>> following output given below. Any help would be appreciated. I am not
>> sure
>> how to exactly determine which atoms are at special positions.
>>
>> Thank you.
>>
>> -Yarrow
>>
>>
>> |-real space refinement
>> (target=simple)---------------------------------------|
>> | start: r_work=0.5500 r_free=0.5441 rmsd: bonds=0.019 angles= 1.68
>> weight= 50|
>> | final: r_work=0.5309 r_free=0.5358 rmsd: bonds=0.029 angles= 2.45
>> weight= 80|
>> |
>> ---------------------------------------------------------------------------
>> |
>>
>> ==================== Compute data/restraints target weights
>> ===================
>>
>> Traceback (most recent call last):
>> File
>> "/usr/bin/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/refine.py",
>> line 11, in <module>
>> command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>> File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/command_line.py",
>> line 159, in run
>> call_back_handler=call_back_handler)
>> File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py",
>> line 1593, in run
>> reference_model_manager = self.reference_model_manager).result
>> File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/strategies.py",
>> line 171, in __init__
>> ion_placement_manager = ion_placement_manager)
>> File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
>> line 87, in __init__
>> self.call(self.weight, "Compute data/restraints target weights")
>> File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
>> line 137, in call
>> func(prefix = prefix)
>> File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
>> line 302, in weight
>> log = self.log)
>> File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weights.py",
>> line 20, in run
>> log = log)
>> File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
>> line 368, in __init__
>> self.xyz_weights_result = self.xyz_weights()
>> File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
>> line 411, in xyz_weights
>> log=self.log)
>> File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
>> line 294, in __init__
>> verbose=0)
>> File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/memory_eraser.py",
>> line 29, in shake_sites
>> max_iterations = max_iterations))
>> File
>> "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
>> line 43, in __init__
>> exception_handling_params=lbfgs_exception_handling_params)
>> File
>> "/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py",
>> line 259, in run
>> log)
>> File
>> "/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py",
>> line 127, in run_c_plus_plus
>> f, g = target_evaluator.compute_functional_and_gradients()
>> File
>> "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
>> line 89, in compute_functional_and_gradients
>> self.apply_shifts()
>> File
>> "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
>> line 70, in apply_shifts
>> site_cart=self.tmp.sites_shifted[i_seq])
>> File
>> "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/__init__.py",
>> line 609, in correct_special_position
>> raise AssertionError(error_message)
>> AssertionError: Excessive special position correction:
>> unit_cell: (56.278, 67.256, 106.26, 90, 90, 90)
>> space_group_info: P 21 2 2
>> special_op: 1/2,y,1/2
>> site_frac: (0.5090941495765681, 0.42722892547242985,
>> 0.5083083194012079)
>> site_special_frac: (0.5, 0.42722892547242985, 0.5)
>> distance_moved: 1.02047
>>
>> Phenix v. 1.8.4-1496
>>
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>
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
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